The Football Association confirmed the defender would face action following a clash with Fulham defender Philippe Senderos.
The incident was not seen by the match officials at Craven Cottage - but was caught on video.
He has until 6pm on Wednesday to respond to the charge.
Speaking after the 1-0 defeat, Stoke boss Tony Pulis refused to be drawn on the incidents involving Huth and team-mate Steven Nzonzi, who caught Bryan Ruiz in the face with a slap.
Pulis said: "I didn't see the elbow on Nzonzi and I did not see that either."